The global COVID-19 pandemic has raised the risk of malnutrition in children under five years, including stunting. Stunting is common in low-income regions, when families cannot afford nutritious meals. Stunting may become more common as a result of changes in family socioeconomic circumstances, personal cleanliness, and environmental sanitation during the pandemic. This study determined the effect of socioeconomic factors and hygiene sanitation during COVID-19 pandemic on the incidence of stunting in coastal areas. This was analytical survey research with cross sectional approach. The total sample was 3886 families who had toddlers aged 0-59 months in the coastal areas in Surabaya City, Indonesia. The study found that low family income, hand-washing habits, clean water sources, sewer access, waste management, and healthy latrine have significant impact to malnutrition, especially stunting.